John,
Akeeba Backup will back up everything in the Joomla! database and every file and folder within the root folder of your site. If your non-Joomla! program uses a separate database, then you need to define that database for Backup.
Restore is a little trickier. Your non-Joomla! program most likely has an equivalent of Joomla!'s configuration.php file. That will need to be manually changed to update the information if you change servers. Without detailed information on the program, I can't be more specific. My CiviCRM program requires manual edits to two files and some custom tweaks to skip temporary and cache data in the backup itself.
Admin Tools will prevent the program from running at all. Keep in mind that all of Joomal!'s URLs are supposed to go through Joomla!'s index.php file. Everything else is blocked. So you will need to create at least one exemption to get the program to run. In the case of my family tree program, I had to exempt the entire directory from Admin Tools. There were too many php files being called to set up separate exemptions for them all.
Dale L. Brackin
Support Specialist
English: native
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!
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